Under the new terms of the contract, Manning will still earn the $40 million in guaranteed money over the next two seasons, but the payouts of those amounts has been tweaked.
Instead of earning $20 million in fully guaranteed base salaries in 2013 and 2014, Manning received a $10 million salary advance and his base salaries in 2013 and 2014 have been lowered to $15 million in each season. The $10 million salary advance is treated like a signing bonus and will be prorated over the next four seasons, reducing Manning's cap number from $20 million to $17.5 million in both 2013 and 2014.
However, the downside to the cap savings the next two seasons is that Manning's cap number will increase by $2.5 million, going from $19 million to $21.5 million, in both 2015 and 2016 as the Broncos will have veered, slightly, from the "pay as you go" approach they had been taking with the 37-year-old quarterback.

when you're paid like this cat is, 2.5 million is drops in the bucket..

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Peyton Manning isn't losing a dime on this transaction, instead he's getting his guaranteed money sooner, while the team gets to spread out the cap hit over more years. It's a good deal for both sides, and it helps the team get some more capspace in their "win now" years with Peyton.